its good that uve read the dependencys for the newer firmwares 
for firmware 1.2.5++ you need cmigner 3.3.2. not 3.3.1
yes, I have 3.3.2 cgminer installed...for firmware 1.2.5++ you need cmigner 3.3.2. not 3.3.1
tell us more what kind jtag did you use and what kind firmware file you use .hex or bin?
upgraded cgminer to 3.4.0 - no any changes.
I have used AVR Dragon, compiled the firmware with Atmel Studio
you make sure program right mcu for your Jal.